Multiple sequence alignment - TraesCS4D01G260100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G260100 chr4D 100.000 5890 0 0 1 5890 429464366 429470255 0.000000e+00 10877
1 TraesCS4D01G260100 chr4B 92.391 5559 258 71 1 5443 527275332 527280841 0.000000e+00 7769
2 TraesCS4D01G260100 chr4B 94.231 260 9 3 5631 5890 527281149 527281402 5.530000e-105 392
3 TraesCS4D01G260100 chr4B 100.000 58 0 0 5588 5645 527281079 527281136 2.240000e-19 108
4 TraesCS4D01G260100 chr4A 89.559 3333 190 82 2652 5890 37065456 37062188 0.000000e+00 4082
5 TraesCS4D01G260100 chr4A 94.584 1311 58 5 514 1816 37067662 37066357 0.000000e+00 2015
6 TraesCS4D01G260100 chr4A 94.289 823 23 6 1814 2617 37066275 37065458 0.000000e+00 1238
7 TraesCS4D01G260100 chr3A 80.131 609 67 25 2850 3432 387283127 387283707 7.110000e-109 405
8 TraesCS4D01G260100 chr7B 79.378 611 68 31 2850 3432 351927612 351927032 1.550000e-100 377
9 TraesCS4D01G260100 chr3B 79.800 500 53 24 2850 3324 385478231 385477755 2.650000e-83 320
10 TraesCS4D01G260100 chr3D 81.890 381 37 13 2850 3210 292037572 292037204 5.770000e-75 292
11 TraesCS4D01G260100 chr1D 79.032 372 47 15 2991 3359 46639592 46639249 5.940000e-55 226
12 TraesCS4D01G260100 chr1A 86.061 165 22 1 83 246 358806238 358806074 6.070000e-40 176
13 TraesCS4D01G260100 chr2A 79.915 234 23 8 2787 3004 733033379 733033154 3.680000e-32 150
14 TraesCS4D01G260100 chrUn 77.481 262 41 12 2752 3003 101291153 101291406 2.210000e-29 141


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G260100 chr4D 429464366 429470255 5889 False 10877.000000 10877 100.000000 1 5890 1 chr4D.!!$F1 5889
1 TraesCS4D01G260100 chr4B 527275332 527281402 6070 False 2756.333333 7769 95.540667 1 5890 3 chr4B.!!$F1 5889
2 TraesCS4D01G260100 chr4A 37062188 37067662 5474 True 2445.000000 4082 92.810667 514 5890 3 chr4A.!!$R1 5376
3 TraesCS4D01G260100 chr3A 387283127 387283707 580 False 405.000000 405 80.131000 2850 3432 1 chr3A.!!$F1 582
4 TraesCS4D01G260100 chr7B 351927032 351927612 580 True 377.000000 377 79.378000 2850 3432 1 chr7B.!!$R1 582

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
548 590 0.603569 ACCTTGACGTAGCACTCCAG 59.396 55.0 0.00 0.0 0.00 3.86 F
1061 1113 0.676782 GGTTCCACAAGCGTATGCCT 60.677 55.0 2.51 0.0 44.31 4.75 F
1569 1622 0.461961 GGAGAGATGAAGGGACACGG 59.538 60.0 0.00 0.0 0.00 4.94 F
1630 1683 0.753262 CTGCTAACATCGCCTAGGGT 59.247 55.0 11.72 0.0 0.00 4.34 F
3461 3655 0.398318 GGGATGGAGGCGCTAAGATT 59.602 55.0 7.64 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1519 0.248498 CCATGTGTAGTCGATCGCGT 60.248 55.0 11.09 1.92 38.98 6.01 R
2254 2414 0.679505 AAAGAGGCTGTAGACACGCA 59.320 50.0 0.00 0.00 0.00 5.24 R
3445 3639 0.034059 CCGAATCTTAGCGCCTCCAT 59.966 55.0 2.29 0.00 0.00 3.41 R
3579 3775 0.738389 GAGAAGGAGAGACTCAGCCG 59.262 60.0 5.02 0.00 31.08 5.52 R
5241 5506 2.009681 AAGGAACCCAACCCATGTTC 57.990 50.0 0.00 0.00 38.08 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.151817 GCTATCCAGGTTCTTGTTCTTGAATT 59.848 38.462 0.00 0.00 0.00 2.17
37 38 5.445069 TCCAGGTTCTTGTTCTTGAATTGA 58.555 37.500 0.00 0.00 0.00 2.57
109 110 4.163427 TCCTTCTCTTCCACATCAAGAGT 58.837 43.478 8.84 0.00 44.99 3.24
137 138 9.956720 CCACTAAGATTGATGACAATAAATTCC 57.043 33.333 0.00 0.00 45.30 3.01
154 158 2.827800 TCCTGTCTCTTGTGCTTCAG 57.172 50.000 0.00 0.00 0.00 3.02
223 227 3.056107 CCTCTGGTAATGAACTTGTCCGA 60.056 47.826 0.00 0.00 0.00 4.55
277 281 4.694509 AGTGAGTGACTGAATTTCATGAGC 59.305 41.667 0.00 0.00 31.75 4.26
291 295 4.919653 GAGCCTGCTCAATCACGA 57.080 55.556 14.07 0.00 42.31 4.35
308 312 1.134401 ACGAAGCGGTCATCCATCATT 60.134 47.619 0.00 0.00 0.00 2.57
331 335 4.675976 TGTTGGTTAGGAGAACGAGAAA 57.324 40.909 0.00 0.00 0.00 2.52
348 352 2.800544 AGAAAACGAGTCATGTTGGTCG 59.199 45.455 0.00 0.06 38.40 4.79
399 403 3.694072 TGGTGACAAACTGAGGACAAAAG 59.306 43.478 0.00 0.00 37.44 2.27
419 423 3.043419 CGGAGGCCGTAGAGATGG 58.957 66.667 0.00 0.00 42.73 3.51
420 424 1.828660 CGGAGGCCGTAGAGATGGT 60.829 63.158 0.00 0.00 42.73 3.55
421 425 1.392710 CGGAGGCCGTAGAGATGGTT 61.393 60.000 0.00 0.00 42.73 3.67
422 426 1.700955 GGAGGCCGTAGAGATGGTTA 58.299 55.000 0.00 0.00 33.76 2.85
423 427 1.614413 GGAGGCCGTAGAGATGGTTAG 59.386 57.143 0.00 0.00 33.76 2.34
424 428 2.584236 GAGGCCGTAGAGATGGTTAGA 58.416 52.381 0.00 0.00 33.76 2.10
425 429 2.554893 GAGGCCGTAGAGATGGTTAGAG 59.445 54.545 0.00 0.00 33.76 2.43
426 430 1.614413 GGCCGTAGAGATGGTTAGAGG 59.386 57.143 0.00 0.00 33.76 3.69
427 431 1.614413 GCCGTAGAGATGGTTAGAGGG 59.386 57.143 0.00 0.00 33.76 4.30
471 503 6.458206 GCACTGTAGACATGAAGAACAACAAA 60.458 38.462 0.00 0.00 0.00 2.83
474 506 7.985184 ACTGTAGACATGAAGAACAACAAACTA 59.015 33.333 0.00 0.00 0.00 2.24
475 507 8.365399 TGTAGACATGAAGAACAACAAACTAG 57.635 34.615 0.00 0.00 0.00 2.57
480 512 9.736023 GACATGAAGAACAACAAACTAGAAAAT 57.264 29.630 0.00 0.00 0.00 1.82
548 590 0.603569 ACCTTGACGTAGCACTCCAG 59.396 55.000 0.00 0.00 0.00 3.86
563 605 4.622220 GCACTCCAGAAATTCATTTGCCAT 60.622 41.667 0.00 0.00 0.00 4.40
617 660 3.958018 TCACTCAGAGAAGGAGTCCTAC 58.042 50.000 13.43 7.45 43.47 3.18
1061 1113 0.676782 GGTTCCACAAGCGTATGCCT 60.677 55.000 2.51 0.00 44.31 4.75
1143 1195 4.193334 CGCGTGCGGGAGATCTGA 62.193 66.667 0.00 0.00 35.56 3.27
1154 1206 1.270571 GGAGATCTGAGAATTCCGGGC 60.271 57.143 0.00 0.00 0.00 6.13
1253 1305 5.594926 ACCGTATATTTCGTAGGAAGTTGG 58.405 41.667 0.00 0.52 32.80 3.77
1343 1395 7.977853 GCATGGTGTTATTTGATTTTCTCATCT 59.022 33.333 0.00 0.00 32.72 2.90
1373 1426 4.638865 GCCGGTAATCATAAGGAAAGTTGT 59.361 41.667 1.90 0.00 0.00 3.32
1466 1519 3.410631 TCTTTGTATGGCGGAACTTCA 57.589 42.857 0.00 0.00 0.00 3.02
1569 1622 0.461961 GGAGAGATGAAGGGACACGG 59.538 60.000 0.00 0.00 0.00 4.94
1594 1647 9.405587 GGAATTCGTTCTTATCATTTTTGTGAA 57.594 29.630 0.00 0.00 0.00 3.18
1601 1654 6.552008 TCTTATCATTTTTGTGAAGGGGTCT 58.448 36.000 0.00 0.00 0.00 3.85
1630 1683 0.753262 CTGCTAACATCGCCTAGGGT 59.247 55.000 11.72 0.00 0.00 4.34
1642 1695 2.308690 GCCTAGGGTGAGAAGTCGTAT 58.691 52.381 11.72 0.00 0.00 3.06
1767 1821 7.010460 GCATTAATTAATGAACTTGCCTGTTCC 59.990 37.037 32.75 12.53 44.40 3.62
1836 1974 9.282247 CACGTAGTAAATTCTACTCGTTATGTT 57.718 33.333 14.52 0.00 41.61 2.71
1848 1986 8.301720 TCTACTCGTTATGTTGTTATGTTGACT 58.698 33.333 0.00 0.00 0.00 3.41
1849 1987 9.563898 CTACTCGTTATGTTGTTATGTTGACTA 57.436 33.333 0.00 0.00 0.00 2.59
1877 2015 1.087771 GGCTACCACACATACCACGC 61.088 60.000 0.00 0.00 0.00 5.34
1880 2018 1.730064 CTACCACACATACCACGCAAC 59.270 52.381 0.00 0.00 0.00 4.17
1978 2119 4.455606 AGTAGAATTAGCCCAATGTCAGC 58.544 43.478 0.00 0.00 0.00 4.26
1991 2148 4.397103 CCAATGTCAGCAATGCTTCTCTTA 59.603 41.667 4.36 0.00 36.40 2.10
2070 2227 3.719871 TCATTTCTACCTACCAGCCAGA 58.280 45.455 0.00 0.00 0.00 3.86
2109 2266 9.131791 CTTACACATATATAAACAAGGGGCTTT 57.868 33.333 0.00 0.00 0.00 3.51
2128 2285 5.476945 GGCTTTGGTTCAAAAGGATCTCTTA 59.523 40.000 0.00 0.00 37.58 2.10
2573 2733 2.203195 TGCCGTGCTGTTTCTGCT 60.203 55.556 0.00 0.00 0.00 4.24
2590 2750 5.801350 TCTGCTATTGTGTATGTTTCTGC 57.199 39.130 0.00 0.00 0.00 4.26
2591 2751 4.329801 TCTGCTATTGTGTATGTTTCTGCG 59.670 41.667 0.00 0.00 0.00 5.18
2611 2772 7.188834 TCTGCGCTGTCTATTTTATGAATTTG 58.811 34.615 9.73 0.00 0.00 2.32
2626 2787 8.755696 TTATGAATTTGCGTAAAGAAAAGCAT 57.244 26.923 4.68 4.57 39.50 3.79
2639 2800 9.249457 GTAAAGAAAAGCATTGCTCTTTTACTT 57.751 29.630 21.97 15.92 42.02 2.24
2643 2804 5.644977 AAGCATTGCTCTTTTACTTACCC 57.355 39.130 12.39 0.00 38.25 3.69
2647 2808 3.323751 TGCTCTTTTACTTACCCGACC 57.676 47.619 0.00 0.00 0.00 4.79
2706 2870 3.777522 TCCCCCACATTTTGTTTGTTTCT 59.222 39.130 0.00 0.00 0.00 2.52
2709 2873 6.070194 TCCCCCACATTTTGTTTGTTTCTTTA 60.070 34.615 0.00 0.00 0.00 1.85
2755 2926 6.220930 GTTGACGCCTATATTGTCCAGATAA 58.779 40.000 0.00 0.00 0.00 1.75
2759 2930 4.081420 CGCCTATATTGTCCAGATAAGGCT 60.081 45.833 8.26 0.00 36.65 4.58
2769 2940 4.954826 GTCCAGATAAGGCTATACGGGTAT 59.045 45.833 0.00 0.00 0.00 2.73
2770 2941 4.954202 TCCAGATAAGGCTATACGGGTATG 59.046 45.833 1.65 0.00 0.00 2.39
3031 3214 4.635473 TCCCCTTCTTGGATATCTTGAGT 58.365 43.478 2.05 0.00 38.35 3.41
3064 3247 4.021894 TGAACTCTGTTGTAGCTTCCTCTC 60.022 45.833 0.00 0.00 0.00 3.20
3077 3260 7.561722 TGTAGCTTCCTCTCTATTCTTGTGTAT 59.438 37.037 0.00 0.00 0.00 2.29
3078 3261 9.069082 GTAGCTTCCTCTCTATTCTTGTGTATA 57.931 37.037 0.00 0.00 0.00 1.47
3079 3262 8.177119 AGCTTCCTCTCTATTCTTGTGTATAG 57.823 38.462 0.00 0.00 0.00 1.31
3205 3394 5.295292 CCAGCACATCCTAAAATAGTGTGAG 59.705 44.000 7.88 0.17 41.93 3.51
3319 3509 2.738846 CGTTCAGATTTGGTGAGTGGAG 59.261 50.000 0.00 0.00 0.00 3.86
3461 3655 0.398318 GGGATGGAGGCGCTAAGATT 59.602 55.000 7.64 0.00 0.00 2.40
3501 3695 4.426112 CGCTCAGAGGCAGTCGCA 62.426 66.667 0.00 0.00 41.24 5.10
3579 3775 1.728490 GGGAATGACGGAGCAATGCC 61.728 60.000 0.00 0.00 0.00 4.40
3626 3822 4.506255 GGCTGGCGGCTGGGTATT 62.506 66.667 19.30 0.00 41.46 1.89
3633 3829 1.101635 GCGGCTGGGTATTTCCTTCC 61.102 60.000 0.00 0.00 36.25 3.46
3636 3835 1.664873 GCTGGGTATTTCCTTCCGTC 58.335 55.000 0.00 0.00 36.25 4.79
3672 3871 0.118346 TCTAACAAGGGGAGGGAGCA 59.882 55.000 0.00 0.00 0.00 4.26
3729 3939 2.209758 GAGAAAAGGGGAGAGGGGATT 58.790 52.381 0.00 0.00 0.00 3.01
3731 3941 1.923148 GAAAAGGGGAGAGGGGATTGA 59.077 52.381 0.00 0.00 0.00 2.57
3732 3942 1.601248 AAAGGGGAGAGGGGATTGAG 58.399 55.000 0.00 0.00 0.00 3.02
3825 4035 6.151480 CCCACCAATGTACGGTTTAGTTTAAT 59.849 38.462 0.00 0.00 33.25 1.40
3868 4089 1.218854 CGGGGGAATACGTTTCGGT 59.781 57.895 0.00 0.00 0.00 4.69
3881 4102 0.533491 TTTCGGTGGGTATCCAGACG 59.467 55.000 11.80 11.80 45.05 4.18
3921 4142 5.068198 GTGTATCTAACCCCTGATACGTCAA 59.932 44.000 0.00 0.00 44.59 3.18
3952 4173 1.336125 GATCCGGGTAACGTAGGTCAG 59.664 57.143 0.00 0.00 42.24 3.51
3968 4189 4.770795 AGGTCAGTACAGATAAATGCACC 58.229 43.478 0.00 0.00 0.00 5.01
4027 4254 7.275920 GTGAATTGAACTGGTAGACATCCTAT 58.724 38.462 0.00 0.00 0.00 2.57
4028 4255 8.421784 GTGAATTGAACTGGTAGACATCCTATA 58.578 37.037 0.00 0.00 0.00 1.31
4124 4351 0.034574 TTGGGGCGCAGATGTTATGT 60.035 50.000 10.83 0.00 0.00 2.29
4203 4438 9.987272 AGAATCTTGTATCGATGTCATAATTCA 57.013 29.630 22.85 7.15 0.00 2.57
4237 4474 4.141251 AGGATAAGTGTGGGTTTGACTTGT 60.141 41.667 0.00 0.00 32.27 3.16
4259 4496 9.522804 CTTGTCTGTGATTACTAATTAGTCCTC 57.477 37.037 21.25 17.79 37.73 3.71
4288 4525 3.645687 AGACTGGATCTAGGATTCCTTGC 59.354 47.826 11.25 0.00 35.15 4.01
4505 4764 9.582431 AAATCTCTGTATTGCTGATGATTTTTG 57.418 29.630 0.00 0.00 34.07 2.44
4692 4951 9.520204 CAAAGTTTCACAGAATTGATGTAAGTT 57.480 29.630 0.00 0.00 0.00 2.66
4802 5061 3.055530 AGGCAATGACTGATCGAGAAGTT 60.056 43.478 4.44 0.00 0.00 2.66
4893 5152 5.994054 CACTCAAAGAAGAAGAACTGATCCA 59.006 40.000 0.00 0.00 0.00 3.41
5115 5380 5.690997 AAAAGCCTACAACTTACAGAAGC 57.309 39.130 0.00 0.00 35.97 3.86
5165 5430 6.090358 GTGAATTTGAATCTCTGCATGGTTTG 59.910 38.462 0.00 0.00 0.00 2.93
5167 5432 2.449464 TGAATCTCTGCATGGTTTGGG 58.551 47.619 0.00 0.00 0.00 4.12
5169 5434 0.032813 ATCTCTGCATGGTTTGGGGG 60.033 55.000 0.00 0.00 0.00 5.40
5206 5471 8.799367 TGAATCTGATGAAATGTTGAATTCTGT 58.201 29.630 7.05 0.00 0.00 3.41
5211 5476 3.640498 TGAAATGTTGAATTCTGTGGGCA 59.360 39.130 7.05 0.00 0.00 5.36
5222 5487 1.811965 TCTGTGGGCAATTGAACGATG 59.188 47.619 10.34 0.00 0.00 3.84
5471 5771 6.864165 TCGCCAGAAAACATGTTTTTAATACC 59.136 34.615 31.42 19.84 42.26 2.73
5511 5811 8.538701 ACATTTTCCCATCATTTAAATGTGCTA 58.461 29.630 23.95 8.61 43.73 3.49
5633 6036 7.987458 ACTATATGAATCACACGTCTTCCAAAT 59.013 33.333 0.00 0.00 0.00 2.32
5695 6098 1.000607 GGAAAAGGAAAGTTGTCGCCC 60.001 52.381 0.00 0.00 0.00 6.13
5754 6157 1.099689 GAGTCCTCTCCTCGGTTCAG 58.900 60.000 0.00 0.00 34.87 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.601857 AGAAGAAGAATTACCAACCCCTCA 59.398 41.667 0.00 0.00 0.00 3.86
37 38 6.713731 TTAGAAGAAGAATTACCAACCCCT 57.286 37.500 0.00 0.00 0.00 4.79
109 110 7.936496 TTTATTGTCATCAATCTTAGTGGCA 57.064 32.000 0.00 0.00 42.45 4.92
137 138 3.577667 CTCTCTGAAGCACAAGAGACAG 58.422 50.000 7.86 0.00 36.66 3.51
154 158 4.576330 TGGAGGAATTTTTCTCCCTCTC 57.424 45.455 13.92 5.91 46.71 3.20
223 227 4.260985 TGAGCATTCCAATTGTATGTCGT 58.739 39.130 15.26 5.14 0.00 4.34
277 281 1.699656 CCGCTTCGTGATTGAGCAGG 61.700 60.000 0.00 0.00 0.00 4.85
291 295 3.091545 ACAAAATGATGGATGACCGCTT 58.908 40.909 0.00 0.00 39.42 4.68
308 312 4.675976 TCTCGTTCTCCTAACCAACAAA 57.324 40.909 0.00 0.00 0.00 2.83
331 335 1.340248 ACTCGACCAACATGACTCGTT 59.660 47.619 0.00 0.00 0.00 3.85
348 352 4.932200 ACCTTCATCAATCTTCGACAACTC 59.068 41.667 0.00 0.00 0.00 3.01
412 416 1.755977 CGCCTCCCTCTAACCATCTCT 60.756 57.143 0.00 0.00 0.00 3.10
413 417 0.676736 CGCCTCCCTCTAACCATCTC 59.323 60.000 0.00 0.00 0.00 2.75
414 418 0.261991 TCGCCTCCCTCTAACCATCT 59.738 55.000 0.00 0.00 0.00 2.90
415 419 0.676736 CTCGCCTCCCTCTAACCATC 59.323 60.000 0.00 0.00 0.00 3.51
416 420 0.760945 CCTCGCCTCCCTCTAACCAT 60.761 60.000 0.00 0.00 0.00 3.55
417 421 1.381327 CCTCGCCTCCCTCTAACCA 60.381 63.158 0.00 0.00 0.00 3.67
418 422 2.134933 CCCTCGCCTCCCTCTAACC 61.135 68.421 0.00 0.00 0.00 2.85
419 423 2.134933 CCCCTCGCCTCCCTCTAAC 61.135 68.421 0.00 0.00 0.00 2.34
420 424 2.282446 CCCCTCGCCTCCCTCTAA 59.718 66.667 0.00 0.00 0.00 2.10
421 425 3.834056 CCCCCTCGCCTCCCTCTA 61.834 72.222 0.00 0.00 0.00 2.43
426 430 3.168528 TATTGCCCCCTCGCCTCC 61.169 66.667 0.00 0.00 0.00 4.30
427 431 2.427753 CTATTGCCCCCTCGCCTC 59.572 66.667 0.00 0.00 0.00 4.70
509 541 9.219603 TCAAGGTTCAAGAAAGAGTACATATTG 57.780 33.333 0.00 0.00 0.00 1.90
510 542 9.220767 GTCAAGGTTCAAGAAAGAGTACATATT 57.779 33.333 0.00 0.00 0.00 1.28
548 590 6.405538 TCCTTTACCATGGCAAATGAATTTC 58.594 36.000 13.04 0.00 0.00 2.17
592 635 3.381272 GGACTCCTTCTCTGAGTGATGAG 59.619 52.174 4.32 9.04 42.94 2.90
617 660 6.040878 CGAATAGGACTGTTGTTAGTTAGGG 58.959 44.000 0.00 0.00 0.00 3.53
877 928 1.265454 GGAGGAGGATTCGGTGGTGT 61.265 60.000 0.00 0.00 0.00 4.16
932 983 2.444895 ATGGTCGAGGAGAGGGGC 60.445 66.667 0.00 0.00 0.00 5.80
939 990 0.031111 AAGGGATGGATGGTCGAGGA 60.031 55.000 0.00 0.00 0.00 3.71
942 993 0.031111 AGGAAGGGATGGATGGTCGA 60.031 55.000 0.00 0.00 0.00 4.20
1061 1113 4.323477 CTGAACCCGCCCACCGAA 62.323 66.667 0.00 0.00 40.02 4.30
1154 1206 1.338200 GGCATGCTAATCCTAGACCGG 60.338 57.143 18.92 0.00 0.00 5.28
1253 1305 3.123050 GTCAAGTGCCAACCATCAAAAC 58.877 45.455 0.00 0.00 0.00 2.43
1332 1384 3.941483 CCGGCACTGTTAGATGAGAAAAT 59.059 43.478 0.00 0.00 0.00 1.82
1343 1395 4.406326 TCCTTATGATTACCGGCACTGTTA 59.594 41.667 0.00 0.00 0.00 2.41
1345 1397 2.769663 TCCTTATGATTACCGGCACTGT 59.230 45.455 0.00 0.00 0.00 3.55
1346 1398 3.469008 TCCTTATGATTACCGGCACTG 57.531 47.619 0.00 0.00 0.00 3.66
1373 1426 5.410439 GCTCACGTAAAATAACCAGAAGGAA 59.590 40.000 0.00 0.00 38.69 3.36
1466 1519 0.248498 CCATGTGTAGTCGATCGCGT 60.248 55.000 11.09 1.92 38.98 6.01
1470 1523 2.320367 GATCGCCATGTGTAGTCGATC 58.680 52.381 7.09 7.09 45.29 3.69
1601 1654 4.564821 GGCGATGTTAGCAGGGGATAAATA 60.565 45.833 0.00 0.00 36.08 1.40
1630 1683 4.832248 AGAAAATGCCATACGACTTCTCA 58.168 39.130 0.00 0.00 0.00 3.27
1642 1695 5.708697 CCATAGCTATCATGAGAAAATGCCA 59.291 40.000 2.34 0.00 0.00 4.92
1688 1741 7.279615 TGACAAGATAAGAGTCCACAAGAAAA 58.720 34.615 0.00 0.00 0.00 2.29
1695 1748 6.151985 TCTCTCTTGACAAGATAAGAGTCCAC 59.848 42.308 22.55 0.00 46.26 4.02
1767 1821 7.178741 CAGATTTCTTAAGAGTTCATTGAGCG 58.821 38.462 5.12 0.00 0.00 5.03
1836 1974 8.492415 AGCCCTATCTTATAGTCAACATAACA 57.508 34.615 0.00 0.00 0.00 2.41
1848 1986 6.666546 GGTATGTGTGGTAGCCCTATCTTATA 59.333 42.308 0.00 0.00 0.00 0.98
1849 1987 5.484290 GGTATGTGTGGTAGCCCTATCTTAT 59.516 44.000 0.00 0.00 0.00 1.73
1877 2015 4.882447 GTTTATCACGAGGATGAACGTTG 58.118 43.478 5.00 0.00 41.03 4.10
1972 2113 4.541973 TCTAAGAGAAGCATTGCTGACA 57.458 40.909 12.82 0.00 39.62 3.58
2109 2266 5.935945 TGTGTAAGAGATCCTTTTGAACCA 58.064 37.500 2.37 0.00 36.34 3.67
2254 2414 0.679505 AAAGAGGCTGTAGACACGCA 59.320 50.000 0.00 0.00 0.00 5.24
2255 2415 1.797025 AAAAGAGGCTGTAGACACGC 58.203 50.000 0.00 0.00 0.00 5.34
2256 2416 3.390135 TGAAAAAGAGGCTGTAGACACG 58.610 45.455 0.00 0.00 0.00 4.49
2573 2733 4.000325 ACAGCGCAGAAACATACACAATA 59.000 39.130 11.47 0.00 0.00 1.90
2590 2750 5.965334 ACGCAAATTCATAAAATAGACAGCG 59.035 36.000 0.00 0.00 43.84 5.18
2591 2751 8.835467 TTACGCAAATTCATAAAATAGACAGC 57.165 30.769 0.00 0.00 0.00 4.40
2611 2772 3.826466 AGAGCAATGCTTTTCTTTACGC 58.174 40.909 9.91 0.00 39.88 4.42
2626 2787 3.071312 TGGTCGGGTAAGTAAAAGAGCAA 59.929 43.478 0.00 0.00 33.94 3.91
2639 2800 1.906574 AGCAAAGAATCTGGTCGGGTA 59.093 47.619 0.00 0.00 0.00 3.69
2643 2804 3.997021 ACTAACAGCAAAGAATCTGGTCG 59.003 43.478 0.00 0.00 34.76 4.79
2647 2808 5.400485 GCAACAACTAACAGCAAAGAATCTG 59.600 40.000 0.00 0.00 36.45 2.90
2685 2849 4.149511 AGAAACAAACAAAATGTGGGGG 57.850 40.909 0.00 0.00 0.00 5.40
2686 2850 7.800155 ATAAAGAAACAAACAAAATGTGGGG 57.200 32.000 0.00 0.00 0.00 4.96
2725 2896 4.523083 ACAATATAGGCGTCAACCAATGT 58.477 39.130 0.00 0.00 0.00 2.71
2734 2905 5.411781 CCTTATCTGGACAATATAGGCGTC 58.588 45.833 0.00 0.00 0.00 5.19
2737 2908 5.428184 AGCCTTATCTGGACAATATAGGC 57.572 43.478 0.00 0.00 38.83 3.93
2755 2926 3.639952 GGTATCCATACCCGTATAGCCT 58.360 50.000 4.57 0.00 45.62 4.58
2769 2940 7.554476 TGAAAAATTGACATATCGTGGTATCCA 59.446 33.333 0.00 0.00 0.00 3.41
2770 2941 7.925993 TGAAAAATTGACATATCGTGGTATCC 58.074 34.615 0.00 0.00 0.00 2.59
3031 3214 6.293407 GCTACAACAGAGTTCAAGCACATTTA 60.293 38.462 7.66 0.00 0.00 1.40
3205 3394 1.301401 TCTACTGTTGCGTGTGCCC 60.301 57.895 0.00 0.00 41.78 5.36
3243 3433 3.643199 TCCCATATGCACTTGCTTGTA 57.357 42.857 2.33 0.00 42.66 2.41
3253 3443 7.779326 TGAGTTTGAGATTTTATCCCATATGCA 59.221 33.333 0.00 0.00 0.00 3.96
3257 3447 7.638444 TGGTGAGTTTGAGATTTTATCCCATA 58.362 34.615 0.00 0.00 0.00 2.74
3260 3450 6.183360 CCATGGTGAGTTTGAGATTTTATCCC 60.183 42.308 2.57 0.00 0.00 3.85
3319 3509 1.141234 GCAGCCACTACTCCGGTAC 59.859 63.158 0.00 0.00 0.00 3.34
3441 3635 1.484444 ATCTTAGCGCCTCCATCCCC 61.484 60.000 2.29 0.00 0.00 4.81
3445 3639 0.034059 CCGAATCTTAGCGCCTCCAT 59.966 55.000 2.29 0.00 0.00 3.41
3461 3655 2.849162 GCCATGATCCCTCCCCGA 60.849 66.667 0.00 0.00 0.00 5.14
3501 3695 1.492176 CCAGATTAGCACCACCATCCT 59.508 52.381 0.00 0.00 0.00 3.24
3537 3733 1.007964 CTAGATCTGAGCGCCACCG 60.008 63.158 2.29 0.00 37.57 4.94
3579 3775 0.738389 GAGAAGGAGAGACTCAGCCG 59.262 60.000 5.02 0.00 31.08 5.52
3585 3781 1.555967 GCACCAGAGAAGGAGAGACT 58.444 55.000 0.00 0.00 0.00 3.24
3626 3822 2.939261 GCTCACCGGACGGAAGGAA 61.939 63.158 18.80 0.00 38.96 3.36
3653 3852 0.118346 TGCTCCCTCCCCTTGTTAGA 59.882 55.000 0.00 0.00 0.00 2.10
3690 3892 1.395826 CGTCTCATCCCTCTGGACCC 61.396 65.000 0.00 0.00 45.58 4.46
3695 3897 3.430098 CCTTTTCTCGTCTCATCCCTCTG 60.430 52.174 0.00 0.00 0.00 3.35
3696 3898 2.763448 CCTTTTCTCGTCTCATCCCTCT 59.237 50.000 0.00 0.00 0.00 3.69
3729 3939 2.262266 TGTGTCCATCCATACCCTCA 57.738 50.000 0.00 0.00 0.00 3.86
3731 3941 1.776667 CCATGTGTCCATCCATACCCT 59.223 52.381 0.00 0.00 0.00 4.34
3732 3942 1.202927 CCCATGTGTCCATCCATACCC 60.203 57.143 0.00 0.00 0.00 3.69
3851 4062 0.745486 CCACCGAAACGTATTCCCCC 60.745 60.000 0.00 0.00 0.00 5.40
3868 4089 2.361119 CGAGAATTCGTCTGGATACCCA 59.639 50.000 0.00 0.00 41.84 4.51
3898 4119 4.795469 TGACGTATCAGGGGTTAGATACA 58.205 43.478 11.66 0.00 44.21 2.29
3947 4168 3.555956 CGGTGCATTTATCTGTACTGACC 59.444 47.826 4.39 0.00 39.61 4.02
3952 4173 3.194861 TCAGCGGTGCATTTATCTGTAC 58.805 45.455 10.38 0.00 0.00 2.90
4124 4351 9.058174 TGAGGAAAAACGAATTTACACTGATAA 57.942 29.630 0.00 0.00 0.00 1.75
4188 4415 6.765512 TGCCATAAAGTGAATTATGACATCGA 59.234 34.615 8.26 0.00 43.05 3.59
4189 4416 6.958255 TGCCATAAAGTGAATTATGACATCG 58.042 36.000 8.26 0.00 43.05 3.84
4190 4417 7.864379 CCTTGCCATAAAGTGAATTATGACATC 59.136 37.037 8.26 0.00 43.05 3.06
4191 4418 7.560991 TCCTTGCCATAAAGTGAATTATGACAT 59.439 33.333 8.26 0.00 43.05 3.06
4203 4438 4.949856 CCACACTTATCCTTGCCATAAAGT 59.050 41.667 0.00 0.00 0.00 2.66
4237 4474 8.904834 GTGAGAGGACTAATTAGTAATCACAGA 58.095 37.037 27.02 11.42 36.50 3.41
4259 4496 6.208599 GGAATCCTAGATCCAGTCTAAGTGAG 59.791 46.154 0.00 0.00 38.91 3.51
4692 4951 5.476945 TCAGTTCATAGTAGCTTCTGTGTGA 59.523 40.000 15.04 9.87 0.00 3.58
4893 5152 4.122046 GCACTTCAAAGGCAACAAATCTT 58.878 39.130 0.00 0.00 41.41 2.40
4954 5214 5.765510 TCTCACATAATTTACAGCCCCAAT 58.234 37.500 0.00 0.00 0.00 3.16
5167 5432 3.881220 TCAGATTCACCGATAAAACCCC 58.119 45.455 0.00 0.00 0.00 4.95
5169 5434 6.677781 TTCATCAGATTCACCGATAAAACC 57.322 37.500 0.00 0.00 0.00 3.27
5170 5435 8.184192 ACATTTCATCAGATTCACCGATAAAAC 58.816 33.333 0.00 0.00 0.00 2.43
5171 5436 8.279970 ACATTTCATCAGATTCACCGATAAAA 57.720 30.769 0.00 0.00 0.00 1.52
5181 5446 9.073368 CACAGAATTCAACATTTCATCAGATTC 57.927 33.333 8.44 0.00 0.00 2.52
5206 5471 2.016318 CTAGCATCGTTCAATTGCCCA 58.984 47.619 0.00 0.00 37.07 5.36
5211 5476 2.991250 AGTGCCTAGCATCGTTCAATT 58.009 42.857 0.00 0.00 41.91 2.32
5241 5506 2.009681 AAGGAACCCAACCCATGTTC 57.990 50.000 0.00 0.00 38.08 3.18
5447 5746 6.866248 AGGTATTAAAAACATGTTTTCTGGCG 59.134 34.615 31.10 0.00 41.45 5.69
5452 5751 9.522804 TGTGTCAGGTATTAAAAACATGTTTTC 57.477 29.630 31.10 19.99 41.45 2.29
5471 5771 4.232221 GGAAAATGTCAGCATTGTGTCAG 58.768 43.478 0.00 0.00 43.89 3.51
5549 5858 9.555727 TTAACTAAAAATCGAATCCCCATAGAG 57.444 33.333 0.00 0.00 0.00 2.43
5550 5859 9.333724 GTTAACTAAAAATCGAATCCCCATAGA 57.666 33.333 0.00 0.00 0.00 1.98
5571 5880 8.250332 TGCCCAGATTTAGATTTGAATGTTAAC 58.750 33.333 0.00 0.00 0.00 2.01
5667 6070 6.756542 CGACAACTTTCCTTTTCCTTTTCATT 59.243 34.615 0.00 0.00 0.00 2.57
5668 6071 6.273071 CGACAACTTTCCTTTTCCTTTTCAT 58.727 36.000 0.00 0.00 0.00 2.57
5669 6072 5.646606 CGACAACTTTCCTTTTCCTTTTCA 58.353 37.500 0.00 0.00 0.00 2.69
5754 6157 3.508840 CTGCGAACGATTGGGGGC 61.509 66.667 0.00 0.00 0.00 5.80
5854 6258 3.319198 GCGTGGGAAGTGGAGGGA 61.319 66.667 0.00 0.00 0.00 4.20


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.